Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 99 of 135
Found at i:30823028 original size:3 final size:3
Alignment explanation
Indices: 30823020--30823053 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
30823010 TTTATATTAT
30823020 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30823054 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30834621 original size:22 final size:21
Alignment explanation
Indices: 30834595--30834637 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
30834585 AAGCAAATGA
* *
30834595 TTTTAAAATTATTATAATTATT
1 TTTTAAAAATA-TAAAATTATT
30834617 TTTTAAAAATATAAAATTATT
1 TTTTAAAAATATAAAATTATT
30834638 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAAAAATATAAAATTATT
Found at i:30834634 original size:21 final size:22
Alignment explanation
Indices: 30834595--30834677 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 22
30834585 AAGCAAATGA
* *
30834595 TTTTAAAATTATTATAATTATT
1 TTTTAAAAATATTAAAATTATT
30834617 TTTTAAAAATA-TAAAATTA--
1 TTTTAAAAATATTAAAATTATT
* *
30834636 --TTAAAATTATTTTAAAATTAAT
1 TTTTAAAA--ATATTAAAATTATT
30834658 TTTT-AAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
30834678 AAAATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
17 6 0.12
19 2 0.04
20 17 0.35
21 9 0.18
22 10 0.20
23 3 0.06
24 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:30834642 original size:9 final size:9
Alignment explanation
Indices: 30834619--30834686 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
30834609 TAATTATTTT
*
30834619 TTAAAAATA
1 TTAAAATTA
30834628 -TAAAATTA
1 TTAAAATTA
30834636 TTAAAATTA
1 TTAAAATTA
30834645 TTTTAAAATTAA
1 --TTAAAATT-A
30834657 TTTTTAAAA-TA
1 ---TTAAAATTA
30834668 -TAAAATTA
1 TTAAAATTA
30834676 TTAAAATTA
1 TTAAAATTA
30834685 TT
1 TT
30834687 TTAATATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.10
8 9 0.18
9 18 0.35
11 9 0.18
12 2 0.04
13 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:30835496 original size:7 final size:7
Alignment explanation
Indices: 30835484--30835531 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
30835474 AGAAGGGGAA
30835484 GAGAAGG
1 GAGAAGG
30835491 GAGAAGG
1 GAGAAGG
30835498 GAGAAGG
1 GAGAAGG
30835505 GAGAAGGG
1 GAGAA-GG
30835513 GATGAAGG
1 GA-GAAGG
30835521 G-GAA-G
1 GAGAAGG
30835526 GAGAAG
1 GAGAAG
30835532 AGGGGAAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.05
6 6 0.16
7 19 0.51
8 7 0.19
9 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (7 bp):
GAGAAGG
Found at i:30835510 original size:21 final size:19
Alignment explanation
Indices: 30835474--30835531 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 19
30835464 AAAAAAAATA
30835474 AGAAGGGGAA-GAGAAGGG
1 AGAAGGGGAAGGAGAAGGG
30835492 AGAAGGGAGAAGGGAGAAGGGG
1 AGAAGGG-GAA-GGAGAA-GGG
30835514 ATGAAGGGGAAGGAGAAG
1 A-GAAGGGGAAGGAGAAG
30835532 AGGGGAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.20
19 3 0.09
20 1 0.03
21 11 0.31
22 7 0.20
23 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.02
Consensus pattern (19 bp):
AGAAGGGGAAGGAGAAGGG
Found at i:30835521 original size:9 final size:8
Alignment explanation
Indices: 30835474--30835523 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 8
30835464 AAAAAAAATA
30835474 AGAAGGGG
1 AGAAGGGG
*
30835482 AAGAGAAGGG
1 -AGA-AGGGG
30835492 AGAA-GGG
1 AGAAGGGG
30835499 AGAA-GGG
1 AGAAGGGG
30835506 AGAAGGGG
1 AGAAGGGG
30835514 ATGAAGGGG
1 A-GAAGGGG
30835523 A
1 A
30835524 AGGAGAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
7 14 0.38
8 5 0.14
9 14 0.38
10 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (8 bp):
AGAAGGGG
Found at i:30835535 original size:23 final size:22
Alignment explanation
Indices: 30835474--30835537 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 22
30835464 AAAAAAAATA
30835474 AGAAGGGGAAGAGAAGGGAGAAGGG
1 AGAA-GGGAAGAG--GGGAGAAGGG
30835499 AGAAGGG-AGAAGGGGATGAAGGG
1 AGAAGGGAAG-AGGGGA-GAAGGG
30835522 -GAAGGAGAAGAGGGGA
1 AGAAGG-GAAGAGGGGA
30835538 AGGAGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
22 9 0.26
23 15 0.43
24 7 0.20
25 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (22 bp):
AGAAGGGAAGAGGGGAGAAGGG
Found at i:30835537 original size:14 final size:14
Alignment explanation
Indices: 30835477--30835543 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
30835467 AAAAATAAGA
30835477 AGGGGAA-GAGAAG
1 AGGGGAAGGAGAAG
*
30835490 -GGAGAAGGGAGAAG
1 AGGGGAA-GGAGAAG
* * *
30835504 -GGAGAAGGGGATG
1 AGGGGAAGGAGAAG
30835517 AAGGGGAAGGAGAAG
1 -AGGGGAAGGAGAAG
30835532 AGGGGAAGGAGA
1 AGGGGAAGGAGA
30835544 TGATGATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 24 0.55
15 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.01
Consensus pattern (14 bp):
AGGGGAAGGAGAAG
Found at i:30835539 original size:29 final size:30
Alignment explanation
Indices: 30835486--30835546 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
30835476 AAGGGGAAGA
*
30835486 GAAGGGAGAAGGGAGAAGGGAGAAGGGGAT
1 GAAGGGAGAAGGGAGAAGGGAGAAGGAGAT
*
30835516 GAAGGG-GAA-GGAGAAGAGGGGAAGGAGAT
1 GAAGGGAGAAGGGAGAAG-GGAGAAGGAGAT
30835545 GA
1 GA
30835547 TGATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 15 0.54
30 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (30 bp):
GAAGGGAGAAGGGAGAAGGGAGAAGGAGAT
Found at i:30844401 original size:4 final size:4
Alignment explanation
Indices: 30844392--30844421 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
30844382 TCGGGATTGA
30844392 CCGC CCGC CCGC CCGC CCGC CCGC CCGC CC
1 CCGC CCGC CCGC CCGC CCGC CCGC CCGC CC
30844422 CCACCGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.77, G:0.23, T:0.00
Consensus pattern (4 bp):
CCGC
Found at i:30845851 original size:18 final size:19
Alignment explanation
Indices: 30845811--30845857 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
30845801 TTTTCTGATA
* *
30845811 ATTTCAATATGCTTCTAGC
1 ATTTCAATATCCTTCAAGC
*
30845830 ATTTCAA-ATCCTTCAAGG
1 ATTTCAATATCCTTCAAGC
*
30845848 ATTTTAATAT
1 ATTTCAATAT
30845858 AAACTTTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (19 bp):
ATTTCAATATCCTTCAAGC
Found at i:30848847 original size:3 final size:3
Alignment explanation
Indices: 30848839--30848870 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30848829 TCAATTCATC
30848839 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30848871 ACTTTGACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30860335 original size:20 final size:21
Alignment explanation
Indices: 30860280--30860355 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 21
30860270 TCAGAAAAAG
*
30860280 TCAACGGTTAA-AGTCAACGA
1 TCAACGGTCAACAGTCAACGA
* **
30860300 TCAAC-ATCAATGGTCAACGA
1 TCAACGGTCAACAGTCAACGA
*
30860320 TCAACGGTCAA-AGTCAATGA
1 TCAACGGTCAACAGTCAACGA
*
30860340 CCAACGGTCAACAGTC
1 TCAACGGTCAACAGTC
30860356 GGTCAACGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.07
20 35 0.76
21 8 0.17
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
TCAACGGTCAACAGTCAACGA
Found at i:30860336 original size:13 final size:13
Alignment explanation
Indices: 30860276--30860336 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
30860266 TTTTTCAGAA
*
30860276 AAAGTCAACGGTT
1 AAAGTCAACGGTC
*
30860289 AAAGTCAACGATC
1 AAAGTCAACGGTC
*
30860302 AACA-TCAATGGTC
1 AA-AGTCAACGGTC
*
30860315 AACGATCAACGGTC
1 AAAG-TCAACGGTC
30860329 AAAGTCAA
1 AAAGTCAA
30860337 TGACCAACGG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 26 0.68
14 12 0.32
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:30866530 original size:18 final size:16
Alignment explanation
Indices: 30866500--30866552 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
30866490 ATTAATCATC
30866500 AAATT-TTTT-TAAAA
1 AAATTATTTTATAAAA
30866514 AATATATATTTTATAAAA
1 AA-AT-TATTTTATAAAA
*
30866532 AAATTGTTTTATATAAA
1 AAATTATTTTATA-AAA
30866549 AAAT
1 AAAT
30866553 GAATATCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 9 0.27
17 13 0.39
18 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTATTTTATAAAA
Found at i:30875118 original size:30 final size:30
Alignment explanation
Indices: 30875052--30875123 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
30875042 TTTTGGATCT
*
30875052 CTTAAAAGTTGGGTAAATTTTTTTAAAATTC
1 CTTAAAAGTT-GGTAAATTTTTTTAAAATCC
**
30875083 CTTAAAAGTTGGTAAATTTTTTTTGAA-CC
1 CTTAAAAGTTGGTAAATTTTTTTAAAATCC
30875112 CTTTAAAAGTTG
1 C-TTAAAAGTTG
30875124 AAAGAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.05
30 25 0.68
31 10 0.27
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
CTTAAAAGTTGGTAAATTTTTTTAAAATCC
Found at i:30883593 original size:21 final size:21
Alignment explanation
Indices: 30883541--30883601 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
30883531 TCAAAAGTTT
* *
30883541 AAAGTTT-AGATTCTAAGATCT
1 AAAGTTTAAGATT-TAAAATCA
* *
30883562 AGAGTTCAAGATTTAAAATCA
1 AAAGTTTAAGATTTAAAATCA
*
30883583 AAAGTTTAAGATTTGAAAT
1 AAAGTTTAAGATTTAAAAT
30883602 TTAAATTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (21 bp):
AAAGTTTAAGATTTAAAATCA
Found at i:30885047 original size:18 final size:18
Alignment explanation
Indices: 30885024--30885060 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30885014 TCCCATATGA
30885024 TCTCACCAAATAATTTAT
1 TCTCACCAAATAATTTAT
30885042 TCTCACCAAATAATTTAT
1 TCTCACCAAATAATTTAT
30885060 T
1 T
30885061 TCTTTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCTCACCAAATAATTTAT
Found at i:30889293 original size:30 final size:29
Alignment explanation
Indices: 30889231--30889293 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
30889221 ATCTATTATC
*
30889231 TTTATAATTTTTAAAGGATTAAATTAAAT
1 TTTATAATTTTTAAAGGATAAAATTAAAT
* *
30889260 TTTATTATTTTTAAGAGGCTAAAATGT-AAT
1 TTTATAATTTTTAA-AGGATAAAAT-TAAAT
30889290 TTTA
1 TTTA
30889294 CCTTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 13 0.45
30 15 0.52
31 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTATAATTTTTAAAGGATAAAATTAAAT
Found at i:30896854 original size:18 final size:19
Alignment explanation
Indices: 30896831--30896867 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30896821 ACTAGTTTAT
*
30896831 TAAATTG-TCAAATTATAA
1 TAAATTGCTCAAAGTATAA
30896849 TAAATTGCTCAAAGTATAA
1 TAAATTGCTCAAAGTATAA
30896868 ATCAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (19 bp):
TAAATTGCTCAAAGTATAA
Found at i:30899842 original size:14 final size:14
Alignment explanation
Indices: 30899805--30899842 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
30899795 TCAACTCAAC
30899805 ATTGAATTTTTTAT
1 ATTGAATTTTTTAT
*
30899819 AGTT-ATTTTTTTAT
1 A-TTGAATTTTTTAT
30899833 ATTGAATTTT
1 ATTGAATTTT
30899843 CTCGTCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.10
14 16 0.80
15 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (14 bp):
ATTGAATTTTTTAT
Found at i:30903721 original size:15 final size:15
Alignment explanation
Indices: 30903678--30903726 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
30903668 TAAACAAACC
*
30903678 TATTAATTATAAT-T
1 TATTAATTAAAATAT
*
30903692 TATTAAATAAAAATAT
1 TATT-AATTAAAATAT
30903708 TATTAATTAAAATAT
1 TATTAATTAAAATAT
30903723 TATT
1 TATT
30903727 TCAAGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.13
15 21 0.70
16 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAATTAAAATAT
Found at i:30903800 original size:43 final size:44
Alignment explanation
Indices: 30903737--30903820 Score: 143
Period size: 43 Copynumber: 1.9 Consensus size: 44
30903727 TCAAGAAAAA
*
30903737 TTTTAAATTTCATATAAAAAAATCTATTAATCTTATTTTATAAT
1 TTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTATAAT
*
30903781 TTTTAAATTTCATAT-AAAAATTCTATTAATCATATTTTAT
1 TTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTAT
30903821 TAAACGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 23 0.61
44 15 0.39
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (44 bp):
TTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTATAAT
Found at i:30907984 original size:19 final size:19
Alignment explanation
Indices: 30907945--30907984 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30907935 ATTATTTCTC
*
30907945 AAAAATAATTTTGGGTCAA
1 AAAAATAATTTTGAGTCAA
* *
30907964 AAAAATACTTTTGAGTTAA
1 AAAAATAATTTTGAGTCAA
30907983 AA
1 AA
30907985 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAAATAATTTTGAGTCAA
Found at i:30912979 original size:15 final size:16
Alignment explanation
Indices: 30912953--30912982 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30912943 CCACCTTTTG
30912953 GAATATTGTTAGATAT
1 GAATATTGTTAGATAT
30912969 GAATA-TGTTAGATA
1 GAATATTGTTAGATA
30912983 CGGCAGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (16 bp):
GAATATTGTTAGATAT
Found at i:30919034 original size:17 final size:17
Alignment explanation
Indices: 30919006--30919039 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30918996 TTTTTCCGTA
30919006 TTAAAAATATATATAATT
1 TTAAAAATATATA-AATT
30919024 TTAAAAA-ATATAAATT
1 TTAAAAATATATAAATT
30919040 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATATAAATT
Found at i:30919045 original size:17 final size:17
Alignment explanation
Indices: 30919007--30919048 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30918997 TTTTCCGTAT
*
30919007 TAAAAATATATATAATTT
1 TAAAAA-ATATATAATTA
30919025 TAAAAAATATA-AATTAA
1 TAAAAAATATATAATT-A
30919042 TAAAAAA
1 TAAAAAA
30919049 ATTCACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATATATAATTA
Found at i:30919238 original size:15 final size:15
Alignment explanation
Indices: 30919218--30919249 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30919208 TTATGTATCA
30919218 TTATATTTTATAAAT
1 TTATATTTTATAAAT
*
30919233 TTATATTTTATATAT
1 TTATATTTTATAAAT
30919248 TT
1 TT
30919250 TTCAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATTTTATAAAT
Found at i:30920036 original size:9 final size:9
Alignment explanation
Indices: 30920022--30920099 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
30920012 ACATATTTAA
*
30920022 AAAAATACT
1 AAAAATAAT
30920031 AAAAATAAT
1 AAAAATAAT
30920040 AAAAA-AATT
1 AAAAATAA-T
30920049 ATAAAGATAA-
1 A-AAA-ATAAT
*
30920059 AAATATAAT
1 AAAAATAAT
**
30920068 AAATTTAATT
1 AAAAATAA-T
*
30920078 AAAAATTAT
1 AAAAATAAT
*
30920087 AAAATTAAT
1 AAAAATAAT
30920096 AAAA
1 AAAA
30920100 CATATTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
8 6 0.11
9 36 0.65
10 10 0.18
11 1 0.02
12 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATAAT
Found at i:30920058 original size:17 final size:17
Alignment explanation
Indices: 30920038--30920089 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
30920028 ACTAAAAATA
30920038 ATAAAAAAATTATAAAG
1 ATAAAAAAATTATAAAG
* * *
30920055 ATAAAAATATAATAAAT
1 ATAAAAAAATTATAAAG
*
30920072 TTAATTAAAAATTATAAA
1 ATAA--AAAAATTATAAA
30920090 ATTAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 17 0.63
19 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAAAAAAATTATAAAG
Found at i:30920094 original size:19 final size:20
Alignment explanation
Indices: 30920055--30920104 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
30920045 AATTATAAAG
*
30920055 ATAAAAATATAATAAATTTA
1 ATAAAAATATAATAAAATTA
30920075 ATTAAAAAT-T-ATAAAATTA
1 A-TAAAAATATAATAAAATTA
30920094 ATAAAACATAT
1 ATAAAA-ATAT
30920105 TTAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 3 0.12
21 7 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAATATAATAAAATTA
Found at i:30920108 original size:29 final size:29
Alignment explanation
Indices: 30920012--30920121 Score: 77
Period size: 29 Copynumber: 3.8 Consensus size: 29
30920002 AAAATAGTAC
* *
30920012 ACATATTTAAAAAAATACTAAAAATAATAAA
1 ACATATTT-AAAAATTA-TAAAATTAATAAA
* *
30920043 A-AAATTATAAAGA-TA-AAAATATAAT-AA
1 ACATATT-TAAAAATTATAAAAT-TAATAAA
** *
30920070 ATTTAATTAAAAATTATAAAATTAATAAA
1 ACATATTTAAAAATTATAAAATTAATAAA
30920099 ACATATTTAAAATATT-TAAAATT
1 ACATATTTAAAA-ATTATAAAATT
30920122 TTATAAAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
27 12 0.19
28 12 0.19
29 25 0.40
30 11 0.18
31 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
ACATATTTAAAAATTATAAAATTAATAAA
Found at i:30920237 original size:29 final size:30
Alignment explanation
Indices: 30920196--30920263 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
30920186 TATTATTGAA
*
30920196 TATTAAAAA-TATTAAAATTGATATAAAT-T
1 TATTAAAAATTATTAAAA-AGATATAAATAT
*
30920225 TA-TAAAAATTATTAAAAAGTTATAAATAT
1 TATTAAAAATTATTAAAAAGATATAAATAT
30920254 TATTAAAAAT
1 TATTAAAAAT
30920264 CTAATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 14 0.41
29 13 0.38
30 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (30 bp):
TATTAAAAATTATTAAAAAGATATAAATAT
Found at i:30920271 original size:49 final size:51
Alignment explanation
Indices: 30920218--30920349 Score: 143
Period size: 49 Copynumber: 2.7 Consensus size: 51
30920208 TAAAATTGAT
*
30920218 ATAAATTTATAAAAATTATTAAAAAGTTATAAATATTATT-AAA-A-ATCTA
1 ATAAATTTATAAAAATTATTAAAAAATTATAAA-ATTATTAAAATATATCTA
* *
30920267 ATAAATTCTAGT--AAATTATTAAAAAATTATGAAATTATTAAAATATATTTA
1 ATAAATT-TA-TAAAAATTATTAAAAAATTATAAAATTATTAAAATATATCTA
* *
30920318 A-AATTTTATAAAAATTA-TAAAAATTTATAAAA
1 ATAAATTTATAAAAATTATTAAAAAATTATAAAA
30920350 ATAATAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
48 7 0.10
49 44 0.63
50 13 0.19
51 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (51 bp):
ATAAATTTATAAAAATTATTAAAAAATTATAAAATTATTAAAATATATCTA
Found at i:30920301 original size:19 final size:19
Alignment explanation
Indices: 30920279--30920365 Score: 76
Period size: 19 Copynumber: 4.6 Consensus size: 19
30920269 AAATTCTAGT
*
30920279 AAATTATTAAAAAATTATG
1 AAATTATTAAAAAATTATA
30920298 AAATTATTAAAATATATT-TA
1 AAATTATTAAAA-A-ATTATA
30920318 AAATT-TTATAAAAATTATA
1 AAATTATTA-AAAAATTATA
* *
30920337 AAAAT-TTATAAAAATAAT-
1 AAATTATTA-AAAAATTATA
30920355 AAATTA-TAAAA
1 AAATTATTAAAA
30920366 TATAACAACT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.05
18 9 0.15
19 34 0.58
20 10 0.17
21 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATTATTAAAAAATTATA
Found at i:30920363 original size:10 final size:9
Alignment explanation
Indices: 30920199--30920365 Score: 83
Period size: 10 Copynumber: 17.6 Consensus size: 9
30920189 TATTGAATAT
30920199 TAAAAA-TA
1 TAAAAATTA
*
30920207 TTAAAATTGA
1 TAAAAATT-A
*
30920217 TATAAATTTA
1 TA-AAAATTA
30920227 TAAAAATTA
1 TAAAAATTA
30920236 TTAAAAAGTTA
1 -TAAAAA-TTA
*
30920247 TAAATATTA
1 TAAAAATTA
30920256 TTAAAAATCTA
1 -TAAAAAT-TA
* *
30920267 -ATAAATTC
1 TAAAAATTA
*
30920275 TAGTAAATTA
1 TA-AAAATTA
30920285 TTAAAAAATTA
1 -T-AAAAATTA
*
30920296 T-GAAATTA
1 TAAAAATTA
*
30920304 TTAAAATATATT
1 -TAAAA-AT-TA
*
30920316 TAAAATTTTA
1 TAAAA-ATTA
30920326 TAAAAATTA
1 TAAAAATTA
30920335 TAAAAATTTA
1 TAAAAA-TTA
30920345 TAAAAA-TA
1 TAAAAATTA
*
30920353 -ATAAATTA
1 TAAAAATTA
30920361 TAAAA
1 TAAAA
30920366 TATAACAACT
Statistics
Matches: 123, Mismatches: 18, Indels: 35
0.70 0.10 0.20
Matches are distributed among these distances:
7 4 0.03
8 16 0.13
9 29 0.24
10 46 0.37
11 26 0.21
12 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
TAAAAATTA
Found at i:30922767 original size:22 final size:21
Alignment explanation
Indices: 30922704--30922772 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
30922694 ACCCATCAAG
*
30922704 CCCAAATCCCATTTAAACCAAA
1 CCCAAAT-TCATTTAAACCAAA
*
30922726 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
30922747 CCCAAATTCATTTAAAACCAAA
1 CCCAAATTCATTT-AAACCAAA
30922769 CCCA
1 CCCA
30922773 TTTAAACCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 25 0.58
22 18 0.42
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:30922785 original size:15 final size:16
Alignment explanation
Indices: 30922755--30922806 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 16
30922745 AACCCAAATT
30922755 CATTTAAAACCAAACC
1 CATTTAAAACCAAACC
30922771 CATTTAAACCTAACCAAACC
1 CATTT-AA---AACCAAACC
*
30922791 CATTTAAAACCTAACC
1 CATTTAAAACCAAACC
30922807 AAACCCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
19 2 0.06
20 14 0.45
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (16 bp):
CATTTAAAACCAAACC
Found at i:30922795 original size:36 final size:37
Alignment explanation
Indices: 30922734--30922806 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
30922724 AACCCACATT
**
30922734 CATTTAAACCAAACCCAAATTCATTTAAAACCAAACC
1 CATTTAAACCAAACCCAAACCCATTTAAAACCAAACC
* *
30922771 CATTTAAACCTAA-CCAAACCCATTTAAAACCTAACC
1 CATTTAAACCAAACCCAAACCCATTTAAAACCAAACC
30922807 AAACCCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.22
Consensus pattern (37 bp):
CATTTAAACCAAACCCAAACCCATTTAAAACCAAACC
Found at i:30922802 original size:21 final size:20
Alignment explanation
Indices: 30922762--30922828 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
30922752 ATTCATTTAA
30922762 AACCAAACCCATTTAAACCT
1 AACCAAACCCATTTAAACCT
30922782 AACCAAACCCATTTAAAACCT
1 AACCAAACCCATTT-AAACCT
* *
30922803 AACCAAACCCATTTGAACCA
1 AACCAAACCCATTTAAACCT
30922823 AACCAA
1 AACCAA
30922829 TTGAACCAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 24 0.55
21 20 0.45
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.16
Consensus pattern (20 bp):
AACCAAACCCATTTAAACCT
Found at i:30922834 original size:14 final size:15
Alignment explanation
Indices: 30922803--30922837 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
30922793 TTTAAAACCT
*
30922803 AACCAAACCCATTTG
1 AACCAAACCCAATTG
30922818 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
30922832 AACCAA
1 AACCAA
30922838 GTCCAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:30922902 original size:7 final size:7
Alignment explanation
Indices: 30922882--30922982 Score: 84
Period size: 7 Copynumber: 15.0 Consensus size: 7
30922872 GTTTGACCGG
30922882 CGTTGAC
1 CGTTGAC
**
30922889 CACTGAC
1 CGTTGAC
30922896 CGTTGAC
1 CGTTGAC
30922903 CGTTGA-
1 CGTTGAC
*
30922909 CTTTGAC
1 CGTTGAC
30922916 CGTTGAC
1 CGTTGAC
**
30922923 CACTGAC
1 CGTTGAC
*
30922930 CGTTG-G
1 CGTTGAC
*
30922936 CTTTGAC
1 CGTTGAC
30922943 CGTTGAC
1 CGTTGAC
*
30922950 CGTTG-G
1 CGTTGAC
*
30922956 CTTTGAC
1 CGTTGAC
30922963 CGTTGA-
1 CGTTGAC
*
30922969 CTTTGAC
1 CGTTGAC
30922976 CGTTGAC
1 CGTTGAC
30922983 TTTTTTTGAA
Statistics
Matches: 70, Mismatches: 20, Indels: 8
0.71 0.20 0.08
Matches are distributed among these distances:
6 18 0.26
7 52 0.74
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.32
Consensus pattern (7 bp):
CGTTGAC
Found at i:30922916 original size:13 final size:13
Alignment explanation
Indices: 30922898--30922985 Score: 89
Period size: 13 Copynumber: 7.2 Consensus size: 13
30922888 CCACTGACCG
30922898 TTGACCGTTGACT
1 TTGACCGTTGACT
*
30922911 TTGACCGTTGACCA
1 TTGACCGTTGA-CT
* *
30922925 CTGACCGTTGGCT
1 TTGACCGTTGACT
30922938 TTGACC---G---
1 TTGACCGTTGACT
*
30922945 TTGACCGTTGGCT
1 TTGACCGTTGACT
30922958 TTGACCGTTGACT
1 TTGACCGTTGACT
30922971 TTGACCGTTGACT
1 TTGACCGTTGACT
30922984 TT
1 TT
30922986 TTTTGAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
7 6 0.10
10 2 0.03
13 44 0.71
14 10 0.16
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:30922917 original size:20 final size:21
Alignment explanation
Indices: 30922882--30922982 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 21
30922872 GTTTGACCGG
**
30922882 CGTTGACCACTGACCGTTGAC
1 CGTTGACCGTTGACCGTTGAC
*
30922903 CGTTGA-CTTTGACCGTTGAC
1 CGTTGACCGTTGACCGTTGAC
** * *
30922923 CACTGACCGTTG-GCTTTGAC
1 CGTTGACCGTTGACCGTTGAC
* *
30922943 CGTTGACCGTTG-GCTTTGAC
1 CGTTGACCGTTGACCGTTGAC
*
30922963 CGTTGA-CTTTGACCGTTGAC
1 CGTTGACCGTTGACCGTTGAC
30922983 TTTTTTTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.06
20 52 0.79
21 10 0.15
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.32
Consensus pattern (21 bp):
CGTTGACCGTTGACCGTTGAC
Found at i:30924031 original size:3 final size:3
Alignment explanation
Indices: 30924019--30924050 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
30924009 TATTCTATTC
30924019 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30924051 GGGATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:30925190 original size:58 final size:58
Alignment explanation
Indices: 30925016--30925193 Score: 277
Period size: 58 Copynumber: 3.1 Consensus size: 58
30925006 AAAATGAGTT
* *
30925016 GTTTATGAATGTTATTT-AGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
* * *
30925074 ATTTATGAGTGTTTTTGAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
* *
30925132 GTTTATTAGTGTTTTTGAAGAATAAAATTATATGTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
30925190 GTTT
1 GTTT
30925194 GTTGATGAGT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 3 0.03
58 106 0.97
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
Found at i:30925456 original size:23 final size:23
Alignment explanation
Indices: 30925413--30925457 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30925403 AAAAAAATTC
**
30925413 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
30925436 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
30925458 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:30927648 original size:20 final size:21
Alignment explanation
Indices: 30927626--30927667 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
30927616 TTTTATTGAT
30927626 AAACTATTATTTTTATTTTTA
1 AAACTATTATTTTTATTTTTA
* *
30927647 AAATTTTTATCTTTTATTTTT
1 AAACTATTAT-TTTTATTTTT
30927668 TAAGTACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
AAACTATTATTTTTATTTTTA
Found at i:30928093 original size:29 final size:28
Alignment explanation
Indices: 30928048--30928125 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
30928038 TTCTATGATT
* *
30928048 TTTTATATTTTTTATAAGTTTATATCAA
1 TTTTATATTTTTAATAAGTTTATATAAA
* *
30928076 TTTTAATATTTTTAATAAATTTTTATAAA
1 TTTT-ATATTTTTAATAAGTTTATATAAA
*
30928105 TTTTATGA-TTTTAATACGTTT
1 TTTTAT-ATTTTTAATAAGTTT
30928126 TTAGAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTTATATTTTTAATAAGTTTATATAAA
Found at i:30928127 original size:39 final size:39
Alignment explanation
Indices: 30928056--30928136 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
30928046 TTTTTTATAT
*
30928056 TTTTTATAAGTTTATATCAATTTTAATATTTTTA-ATAAA
1 TTTTTATAAATTTATATCAATTTTAATATTTTTAGA-AAA
*
30928095 TTTTTATAAATTT-TAT-GATTTTAATACGTTTTTAGAAAA
1 TTTTTATAAATTTATATCAATTTTAATA--TTTTTAGAAAA
30928134 TTT
1 TTT
30928137 AAAATATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 9 0.24
38 3 0.08
39 24 0.65
40 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (39 bp):
TTTTTATAAATTTATATCAATTTTAATATTTTTAGAAAA
Found at i:30928663 original size:5 final size:5
Alignment explanation
Indices: 30928655--30928680 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30928645 GAGATAGAAT
30928655 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
30928681 ATATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:30928920 original size:33 final size:34
Alignment explanation
Indices: 30928883--30928954 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
30928873 AGTAAACAAC
* *
30928883 ATTTGGGTAAGGTAAAAGATAAAAAATT-AAAAT
1 ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
*
30928916 ATTTGGATAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
30928950 ATTTG
1 ATTTG
30928955 AGTTTAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 25 0.71
34 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (34 bp):
ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
Found at i:30931559 original size:13 final size:13
Alignment explanation
Indices: 30931541--30931582 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
30931531 GATTTGAAGG
30931541 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
30931554 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
*
30931567 AAGAAAGAAGGAAGA
1 AA-AAA-AAGAAAGA
30931582 A
1 A
30931583 GAAGAACGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 15 0.58
14 3 0.12
15 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:30931567 original size:17 final size:16
Alignment explanation
Indices: 30931541--30931572 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30931531 GATTTGAAGG
30931541 AAAAAAAGAAAGAAAA
1 AAAAAAAGAAAGAAAA
30931557 AAAAGAAAGAAAGAAA
1 AAAA-AAAGAAAGAAA
30931573 GAAGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAGAAAA
Found at i:30931759 original size:18 final size:18
Alignment explanation
Indices: 30931736--30931770 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30931726 GGAAGAAATG
30931736 TAAGTTTGCTTAATTTTT
1 TAAGTTTGCTTAATTTTT
*
30931754 TAAGTTTGGTTAATTTT
1 TAAGTTTGCTTAATTTT
30931771 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGCTTAATTTTT
Found at i:30931850 original size:35 final size:34
Alignment explanation
Indices: 30931751--30931851 Score: 87
Period size: 35 Copynumber: 2.8 Consensus size: 34
30931741 TTGCTTAATT
* *
30931751 TTTTAAGTTTGGTTAATTTTAAATTTAATTTTAAATA
1 TTTTAA-TTT-GTTAA-TTTAATTTTTATTTTAAATA
* *
30931788 TTTTAATTTGTTAA-TTAATTTGATTATTTTAAGTT
1 TTTTAATTTGTTAATTTAATTT--TTATTTTAAATA
**
30931823 TTTTGTTTTGTTTAATTTAATTTTTATTT
1 TTTTAATTTG-TTAATTTAATTTTTATTT
30931852 GATTTGTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 6 0.11
35 28 0.52
36 7 0.13
37 13 0.24
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (34 bp):
TTTTAATTTGTTAATTTAATTTTTATTTTAAATA
Found at i:30931856 original size:11 final size:12
Alignment explanation
Indices: 30931837--30931874 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
30931827 GTTTTGTTTA
30931837 ATTTAATTT-TT
1 ATTTAATTTGTT
*
30931848 ATTTGATTTGTT
1 ATTTAATTTGTT
30931860 ATTTAATGTTGTT
1 ATTTAAT-TTGTT
30931873 AT
1 AT
30931875 AGTTGAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 8 0.35
13 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (12 bp):
ATTTAATTTGTT
Found at i:30931873 original size:13 final size:12
Alignment explanation
Indices: 30931789--30931874 Score: 56
Period size: 12 Copynumber: 7.1 Consensus size: 12
30931779 TTTTAAATAT
30931789 TTTAATTTGTTA
1 TTTAATTTGTTA
*
30931801 ATTAATTTGATTA
1 TTTAATTTG-TTA
30931814 TTTTAAGTTT-TT-
1 -TTTAA-TTTGTTA
*
30931826 TGT--TTTGTTTAA
1 TTTAATTTG-TT-A
30931838 TTTAATTT-TTA
1 TTTAATTTGTTA
*
30931849 TTTGATTTGTTA
1 TTTAATTTGTTA
30931861 TTTAATGTTGTTA
1 TTTAAT-TTGTTA
30931874 T
1 T
30931875 AGTTGAGTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
8 3 0.05
10 2 0.04
11 10 0.18
12 20 0.35
13 12 0.21
14 7 0.12
15 3 0.05
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.66
Consensus pattern (12 bp):
TTTAATTTGTTA
Found at i:30934368 original size:45 final size:45
Alignment explanation
Indices: 30934297--30934388 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
30934287 CCCTAGCTCA
30934297 TCAAGCCAAGGATATCAGCTTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCTTCAGTTTGACGAGCCACCGCAATAC
* * * *
30934342 TCAAGCCAAGGATATTAGGTTGAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAGCTTCAGTTTGACGAGCCACCGCAATAC
30934387 TC
1 TC
30934389 TACTCCTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCTTCAGTTTGACGAGCCACCGCAATAC
Found at i:30934666 original size:28 final size:27
Alignment explanation
Indices: 30934635--30934700 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
30934625 TTAAACCCTA
*
30934635 AAACCTAAATCC-AAAACCCTAGACTTGG
1 AAACCTAAA-CCTAAAACCCTAAACTT-G
* *
30934663 AAACATAAACCTTAAACCCTAAACTTG
1 AAACCTAAACCTAAAACCCTAAACTTG
*
30934690 AACCCTAAACC
1 AAACCTAAACC
30934701 CTATACATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (27 bp):
AAACCTAAACCTAAAACCCTAAACTTG
Found at i:30937718 original size:4 final size:4
Alignment explanation
Indices: 30937709--30937748 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
30937699 ATTTTTCTCC
30937709 TTCT TTCT TTCT TTCCT TT-T TTCTT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TT-CT TTCT TTC-T TTCT TTCT TTCT TTC
30937749 CCGTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 22 0.67
5 8 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:30937737 original size:25 final size:26
Alignment explanation
Indices: 30937700--30937749 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
30937690 ACACATTACA
30937700 TTTTTCTCCTTCTTTCTTTCTTTCCT
1 TTTTTCTCCTTCTTTCTTTCTTTCCT
*
30937726 TTTTTCT-TTTCTTTCTTTCTTTCC
1 TTTTTCTCCTTCTTTCTTTCTTTCC
30937750 CGTTTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTCTCCTTCTTTCTTTCTTTCCT
Found at i:30939520 original size:40 final size:40
Alignment explanation
Indices: 30939445--30939520 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
30939435 GAAATAAATA
*
30939445 AAAAGAAATTATGAAAATTATAACAAATTATAATAATGCT
1 AAAAGAAATTATGAAAATTATAACAAAATATAATAATGCT
30939485 AAAAGAATATTTAT-AAAAGTTATAA-AAAATA-AATAA
1 AAAAGAA-A-TTATGAAAA-TTATAACAAAATATAATAA
30939521 AATATTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 12 0.38
41 10 0.31
42 10 0.31
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.29
Consensus pattern (40 bp):
AAAAGAAATTATGAAAATTATAACAAAATATAATAATGCT
Found at i:30943609 original size:57 final size:59
Alignment explanation
Indices: 30943495--30943612 Score: 143
Period size: 63 Copynumber: 2.0 Consensus size: 59
30943485 CTTGAAGAAT
* *
30943495 TAAGCTGTTAGTTTCTAAGAATTAGTTGTAAATTAGAAAAGAAAAACATGTGTAACCTCTGAA
1 TAAGCTGTTAGTTTCTAAGAATTAGTTG-AAATT---AAAGAAAAACAAGTCTAACCTCTGAA
*
30943558 TAAGCTGTTAGTTTCTAAGAATTAGTTCG-AATT-TAG-AAAACAAGTCTAACCTCTG
1 TAAGCTGTTAGTTTCTAAGAATTAGTT-GAAATTAAAGAAAAACAAGTCTAACCTCTG
30943613 CTTTGTCCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
57 17 0.33
58 2 0.04
62 4 0.08
63 27 0.53
64 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (59 bp):
TAAGCTGTTAGTTTCTAAGAATTAGTTGAAATTAAAGAAAAACAAGTCTAACCTCTGAA
Found at i:30946561 original size:2 final size:2
Alignment explanation
Indices: 30946554--30946591 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30946544 TTTAATTTGA
30946554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30946592 TTGTAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30950542 original size:23 final size:23
Alignment explanation
Indices: 30950512--30950558 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30950502 AGTTATGTTC
30950512 AAGCAAAAAAGCAAATTAAATGA
1 AAGCAAAAAAGCAAATTAAATGA
30950535 AAGCAAAAAAGCAAATTAAATGA
1 AAGCAAAAAAGCAAATTAAATGA
30950558 A
1 A
30950559 CTTTCTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (23 bp):
AAGCAAAAAAGCAAATTAAATGA
Found at i:30954803 original size:15 final size:15
Alignment explanation
Indices: 30954779--30954808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30954769 TATGTGTATG
30954779 TATTTATTTATTATT
1 TATTTATTTATTATT
*
30954794 TATTTGTTTATTATT
1 TATTTATTTATTATT
30954809 CATTAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:30954887 original size:23 final size:23
Alignment explanation
Indices: 30954820--30954887 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
30954810 ATTAACATTA
*
30954820 TTCGTGAACACGTTCAATTATATG
1 TTCGTGAACATGTTCAATTA-ATG
* **
30954844 TTCATGAACATGTTCGTTTAATG
1 TTCGTGAACATGTTCAATTAATG
* *
30954867 TTCGTGAATATGTTTAATTAA
1 TTCGTGAACATGTTCAATTAA
30954888 GTTAAATAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (23 bp):
TTCGTGAACATGTTCAATTAATG
Found at i:30959735 original size:21 final size:21
Alignment explanation
Indices: 30959711--30959786 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
30959701 GAAATTTAAA
30959711 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
* *
30959732 ACAAAACCTTATGAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
*
30959754 ACAAACATTATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
30959775 ACAAACATAATG
1 ACAAACATAATG
30959787 TTTTGTAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 31 0.62
22 19 0.38
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:30959745 original size:22 final size:22
Alignment explanation
Indices: 30959713--30959779 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
30959703 AATTTAAAAC
*
30959713 AAACATAATGAGGAGAGTTACA
1 AAACATTATGAGGAGAGTTACA
*
30959735 AAACCTTATGAGGAGAGTTAC-
1 AAACATTATGAGGAGAGTTACA
30959756 AAACATTATGAGGAGAGTTACA
1 AAACATTATGAGGAGAGTTACA
30959778 AA
1 AA
30959780 CATAATGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.49
22 21 0.51
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.21
Consensus pattern (22 bp):
AAACATTATGAGGAGAGTTACA
Found at i:30965983 original size:19 final size:19
Alignment explanation
Indices: 30965950--30965997 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
30965940 CTTTAAATTG
* * *
30965950 TTTTAAAATTGTTTTTATTT
1 TTTTAAAA-TCTTTTAATAT
*
30965970 TTTTTAAATCTTTTAATAT
1 TTTTAAAATCTTTTAATAT
30965989 TTTTAAAAT
1 TTTTAAAAT
30965998 TTGGTCACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTAAAATCTTTTAATAT
Found at i:30974073 original size:27 final size:27
Alignment explanation
Indices: 30974025--30974077 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
30974015 ACACATGAGT
* *
30974025 GGTGCCATGTTGAGTGGTGGCACCAAA
1 GGTGCCATGTTAAGTGGCGGCACCAAA
* *
30974052 GGTGCCATTTTAATTGGCGGCACCAA
1 GGTGCCATGTTAAGTGGCGGCACCAA
30974078 GGGATCCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (27 bp):
GGTGCCATGTTAAGTGGCGGCACCAAA
Found at i:30974162 original size:24 final size:24
Alignment explanation
Indices: 30974130--30974176 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
30974120 ATGTGGAACC
*
30974130 AGTAGAAAATGAAGATTCAACTCT
1 AGTAGAAAATGAAGATCCAACTCT
30974154 AGTAGAAAATGAAGATCCAACTC
1 AGTAGAAAATGAAGATCCAACTC
30974177 CGTGTATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (24 bp):
AGTAGAAAATGAAGATCCAACTCT
Found at i:30983937 original size:10 final size:11
Alignment explanation
Indices: 30983924--30983969 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
30983914 AAAAAATCAC
30983924 AAAAAG-AAAG
1 AAAAAGAAAAG
30983934 AAAAAG-AAAG
1 AAAAAGAAAAG
*
30983944 AAGAAGAAAAG
1 AAAAAGAAAAG
30983955 AGAAAAGAAAAG
1 A-AAAAGAAAAG
30983967 AAA
1 AAA
30983970 TATATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:30987205 original size:14 final size:14
Alignment explanation
Indices: 30987186--30987254 Score: 68
Period size: 14 Copynumber: 5.0 Consensus size: 14
30987176 GGATCCGATT
*
30987186 TTAAACCTTAAACC
1 TTAAACCCTAAACC
*
30987200 TTAAACCCTAAACA
1 TTAAACCCTAAACC
* **
30987214 TAAAATACTAAACC
1 TTAAACCCTAAACC
30987228 TTAAACCCTAAA-C
1 TTAAACCCTAAACC
* *
30987241 ATAAACACTAAACC
1 TTAAACCCTAAACC
30987255 ATATGAGAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
13 11 0.26
14 32 0.74
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
TTAAACCCTAAACC
Found at i:30987226 original size:28 final size:27
Alignment explanation
Indices: 30987194--30987254 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
30987184 TTTTAAACCT
*
30987194 TAAACCTTAAACCCTAAACATAAAATAC
1 TAAACCTTAAACCCTAAACAT-AAACAC
30987222 TAAACCTTAAACCCTAAACATAAACAC
1 TAAACCTTAAACCCTAAACATAAACAC
30987249 TAAACC
1 TAAACC
30987255 ATATGAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (27 bp):
TAAACCTTAAACCCTAAACATAAACAC
Found at i:30995314 original size:24 final size:21
Alignment explanation
Indices: 30995286--30995327 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
30995276 ACTTACTTAC
30995286 TTAC-TACTAACAAAATAAAA
1 TTACTTACTAACAAAATAAAA
30995306 TTACTTACTAACAAAATAAAA
1 TTACTTACTAACAAAATAAAA
30995327 T
1 T
30995328 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
TTACTTACTAACAAAATAAAA
Found at i:30995652 original size:12 final size:12
Alignment explanation
Indices: 30995637--30995667 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
30995627 CTAACAAATT
*
30995637 AAATAACTTTAA
1 AAATAAATTTAA
30995649 AAATAAATTTAA
1 AAATAAATTTAA
30995661 AAATAAA
1 AAATAAA
30995668 CACACAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:30995717 original size:3 final size:3
Alignment explanation
Indices: 30995709--30995843 Score: 73
Period size: 3 Copynumber: 43.3 Consensus size: 3
30995699 TAAAATAACT
* *
30995709 TTC TTC TTC TTC TTC TT- TTC TTT TTCC TCC TTC TTTC TTTC TTTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC -TTC -TTC -TTC -TTC
* * * *
30995758 TT- TCC TT- TCC TTC TTC TTC TTC TTC TTC TTCC TCC TCC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC -TTC
* *
30995803 TTTC TTTC TTTC TT- TCC TT- TCC TTC TTC TTC TTC TTC TTC T
1 -TTC -TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
30995844 CCTGTAGCTG
Statistics
Matches: 109, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.06
3 70 0.64
4 33 0.30
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:30995814 original size:57 final size:57
Alignment explanation
Indices: 30995707--30995843 Score: 242
Period size: 57 Copynumber: 2.4 Consensus size: 57
30995697 AATAAAATAA
**
30995707 CTTT-CTTCTTCTTCTTCTT-TTCTTTTTCCTCCTTCTTTCTTTCTTTCTTTCTTTC
1 CTTTCCTTCTTCTTCTTCTTCTTCTTCCTCCTCCTTCTTTCTTTCTTTCTTTCTTTC
30995762 CTTTCCTTCTTCTTCTTCTTCTTCTTCCTCCTCCTTCTTTCTTTCTTTCTTTCTTTC
1 CTTTCCTTCTTCTTCTTCTTCTTCTTCCTCCTCCTTCTTTCTTTCTTTCTTTCTTTC
30995819 CTTTCCTTCTTCTTCTTCTTCTTCT
1 CTTTCCTTCTTCTTCTTCTTCTTCT
30995844 CCTGTAGCTG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
55 4 0.05
56 15 0.19
57 59 0.76
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (57 bp):
CTTTCCTTCTTCTTCTTCTTCTTCTTCCTCCTCCTTCTTTCTTTCTTTCTTTCTTTC
Found at i:30995824 original size:5 final size:4
Alignment explanation
Indices: 30995739--30995829 Score: 75
Period size: 4 Copynumber: 23.2 Consensus size: 4
30995729 TTTTTCCTCC
*
30995739 TTCT TTCT TTCT TTCT TTCT TTCCT TTCC TTC- TTC- TTC- TTC- TTC-
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT
* * * *
30995783 TTCT TCCT CCTCC TTCT TTCT TTCT TTCT TTCT TTCCT TTCC TTCT T
1 TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT T
30995830 CTTCTTCTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
3 15 0.20
4 50 0.68
5 9 0.12
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTCT
Found at i:30997748 original size:21 final size:22
Alignment explanation
Indices: 30997722--30997815 Score: 74
Period size: 22 Copynumber: 4.4 Consensus size: 22
30997712 AAAAATAACT
*
30997722 AATAAATAAAA-TACATAAAAC
1 AATAAATAAAATTAAATAAAAC
30997743 AATAAATAAAATTAAATAAAAGC
1 AATAAATAAAATTAAATAAAA-C
* *
30997766 AA-AATTGTAAATGTAAAT--AA-
1 AATAAAT-AAAAT-TAAATAAAAC
*
30997786 AATAAATAAACAATAAAT-AAAC
1 AATAAATAAA-ATTAAATAAAAC
30997808 AATAAATA
1 AATAAATA
30997816 TATGAAATGC
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
20 9 0.15
21 17 0.29
22 21 0.36
23 7 0.12
24 5 0.08
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (22 bp):
AATAAATAAAATTAAATAAAAC
Found at i:30997800 original size:11 final size:11
Alignment explanation
Indices: 30997786--30997815 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
30997776 ATGTAAATAA
30997786 AATAAATAAAC
1 AATAAATAAAC
30997797 AATAAATAAAC
1 AATAAATAAAC
30997808 AATAAATA
1 AATAAATA
30997816 TATGAAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAAATAAAC
Found at i:30997878 original size:19 final size:19
Alignment explanation
Indices: 30997856--30997922 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
30997846 TTAGGCATGA
30997856 AAATAAATGACAAATAAAT
1 AAATAAATGACAAATAAAT
* *
30997875 AAATAAA-CAAACAATAAAT
1 AAATAAATGACA-AATAAAT
* *
30997894 AAATTAAATGTCAAAATAAAC
1 AAA-TAAATGAC-AAATAAAT
30997915 AAATAAAT
1 AAATAAAT
30997923 ATAATTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
19 17 0.45
20 9 0.24
21 9 0.24
22 1 0.03
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (19 bp):
AAATAAATGACAAATAAAT
Found at i:31002064 original size:36 final size:36
Alignment explanation
Indices: 31002017--31002090 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
31002007 TCAAAGAGCA
31002017 AAAATTTTGAAAACAACTACAAAATCCTACCGGTAG
1 AAAATTTTGAAAACAACTACAAAATCCTACCGGTAG
* *
31002053 AAAATTTTGAAAACAACTACAGAATCCTATCGGTAG
1 AAAATTTTGAAAACAACTACAAAATCCTACCGGTAG
31002089 AA
1 AA
31002091 CTGGTAGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (36 bp):
AAAATTTTGAAAACAACTACAAAATCCTACCGGTAG
Found at i:31002639 original size:21 final size:21
Alignment explanation
Indices: 31002608--31002683 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
31002598 CAGTAGCAGA
* *
31002608 CTTCTATCGATACTTGTGATG
1 CTTCTACCGATACTAGTGATG
* * *
31002629 GTTCTACCGATACAAGTG-TAC
1 CTTCTACCGATACTAGTGAT-G
* *
31002650 CTTCTACCGATACTCGAGATG
1 CTTCTACCGATACTAGTGATG
31002671 CTTCTACCGATAC
1 CTTCTACCGATAC
31002684 AAAAAACTCC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (21 bp):
CTTCTACCGATACTAGTGATG
Found at i:31003428 original size:18 final size:18
Alignment explanation
Indices: 31003383--31003449 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
31003373 GAATGCTCTT
* *
31003383 ACGAGCCGGTATGCTCTA
1 ACGAGCCAGTATGCTCAA
** *
31003401 ATAAGTCAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
*
31003419 ACGAGCCAGTATGCTCCA
1 ACGAGCCAGTATGCTCAA
* *
31003437 ATGAGCTAGTATG
1 ACGAGCCAGTATG
31003450 TTAATCCTTC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (18 bp):
ACGAGCCAGTATGCTCAA
Found at i:31006468 original size:18 final size:18
Alignment explanation
Indices: 31006442--31006480 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31006432 TTGATCTAGA
* *
31006442 TAATAATTCCCATCAATT
1 TAATAATTCCAATAAATT
*
31006460 TAATCATTCCAATAAATT
1 TAATAATTCCAATAAATT
31006478 TAA
1 TAA
31006481 ATATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATTCCAATAAATT
Found at i:31019021 original size:34 final size:34
Alignment explanation
Indices: 31018931--31019022 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
31018921 TTGCAACCTT
*
31018931 CAAAGATTCTTTG-GAAGAAAAGATGGAGATGAA
1 CAAAGATTCTTTGCAAAGAAAAGATGGAGATGAA
* * * *
31018964 CAGAAGTGGTTCTCTGCAAAGAAAAGATGGAGATTAG
1 CA-AA--GATTCTTTGCAAAGAAAAGATGGAGATGAA
*
31019001 TAAAGATTCTTTGCAAAGAAAA
1 CAAAGATTCTTTGCAAAGAAAA
31019023 ATAAAGAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
33 2 0.04
34 18 0.38
36 9 0.19
37 18 0.38
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (34 bp):
CAAAGATTCTTTGCAAAGAAAAGATGGAGATGAA
Found at i:31019240 original size:29 final size:29
Alignment explanation
Indices: 31019204--31019268 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
31019194 ATAAATTTAG
*
31019204 AATTTAGTCTTTATACTTTTATT-TTTAAA
1 AATTTAGTCTCTATA-TTTTATTATTTAAA
* * *
31019233 AATTTAGTCTCTCTATTTTTTTATTTCAA
1 AATTTAGTCTCTATATTTTATTATTTAAA
31019262 AATTTAG
1 AATTTAG
31019269 GTCCAACTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (29 bp):
AATTTAGTCTCTATATTTTATTATTTAAA
Found at i:31022388 original size:3 final size:3
Alignment explanation
Indices: 31022374--31022409 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
31022364 ATCACCACTG
*
31022374 TCA TCG TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
31022410 CTGCCATCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:31025332 original size:16 final size:16
Alignment explanation
Indices: 31025290--31025337 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
31025280 TTCTAGTCCA
31025290 TTAAATTTATAATATT
1 TTAAATTTATAATATT
*
31025306 TTGAATTTAT-ATATAT
1 TTAAATTTATAATAT-T
*
31025322 TTAAATGTATAA-ATT
1 TTAAATTTATAATATT
31025337 T
1 T
31025338 GTTACTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 6 0.22
16 20 0.74
17 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
TTAAATTTATAATATT
Found at i:31027290 original size:23 final size:23
Alignment explanation
Indices: 31027262--31027314 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
31027252 AGATTCTTAT
31027262 ATGTAA-AAAAT-AGAAATAAATTA
1 ATGTAATAAAATGA-AAAT-AATTA
*
31027285 ATGTAATATAATGAAAATAATTA
1 ATGTAATAAAATGAAAATAATTA
31027308 ATGTAAT
1 ATGTAAT
31027315 TTTATTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 18 0.67
24 8 0.30
25 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (23 bp):
ATGTAATAAAATGAAAATAATTA
Found at i:31029874 original size:194 final size:194
Alignment explanation
Indices: 31029470--31029914 Score: 549
Period size: 194 Copynumber: 2.3 Consensus size: 194
31029460 GAAACCGACA
* * * * *
31029470 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCAATAGCTTTTGTGAGTAGCATCGTGAGTCG
1 CGATGGATGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTTATGTGAGCAGCATCATGAGTCG
* * *
31029535 AAAAAGAGATATGAAATCCTAAAATAGATTACAGGCCCTAAGATGGCTGGGATTTATGCTTGAAT
66 AAAAAGAGATATGAAATCCTAAAATAGATTACAGGCCCTAAGATGGCTGAGACTTATGCATGAAT
** * * * * * * *
31029600 GCTATTCTCGACAACTCGTGTGAGCAGTATCGTTAGGGAACAGTTATATGCATAGATACCATAT
131 GCTACACCCAACAACTCGTGTGAGCAGCATCATTAGGGAACAGTTATATGCACAGACACCATAC
* * * * *
31029664 CGATGGCTGAGGTACCGCATATGTTGCGACTCCTCGACAGCTTGTGTGAGCAGCGTCATGAGTCA
1 CGATGGATGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTTATGTGAGCAGCATCATGAGTC-
* *
31029729 GAAAAAGAGATATG-AATCCTAAAATGGATTACAGGCCCTACGATGGCTGAGACTTATGCAT-AA
65 GAAAAAGAGATATGAAATCCTAAAATAGATTACAGGCCCTAAGATGGCTGAGACTTATGCATGAA
* *
31029792 GTGCATACACCCAACAGCTCGTGTGAGCAGCATCATTA-GGAGACAGTT-TATAG-ACAGACATC
130 -TGC-TACACCCAACAACTCGTGTGAGCAGCATCATTAGGGA-ACAGTTATAT-GCACAGACACC
*
31029854 GTAC
191 ATAC
* *
31029858 CGATGGATGTGGTACCGCATATGTTGCGAGTCCTCGATAGCTCATGTGAGCAGCATC
1 CGATGGATGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTTATGTGAGCAGCATC
31029915 GAGTACTGGT
Statistics
Matches: 214, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
193 2 0.01
194 165 0.77
195 47 0.22
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (194 bp):
CGATGGATGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTTATGTGAGCAGCATCATGAGTCG
AAAAAGAGATATGAAATCCTAAAATAGATTACAGGCCCTAAGATGGCTGAGACTTATGCATGAAT
GCTACACCCAACAACTCGTGTGAGCAGCATCATTAGGGAACAGTTATATGCACAGACACCATAC
Found at i:31031569 original size:21 final size:21
Alignment explanation
Indices: 31031524--31031579 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
31031514 ATGTGCAGAT
* * *
31031524 TTCTACCGATACAAGTGATAG
1 TTCTACCGATACTAGTCATAC
*
31031545 TTCTACCGATACTAGTCTTAC
1 TTCTACCGATACTAGTCATAC
*
31031566 TTCTATCGATACTA
1 TTCTACCGATACTA
31031580 AAAACTCTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (21 bp):
TTCTACCGATACTAGTCATAC
Found at i:31031817 original size:13 final size:13
Alignment explanation
Indices: 31031795--31031825 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31031785 TTCATACCAG
*
31031795 TTCATTCACAAAT
1 TTCATACACAAAT
31031808 TTCATACACAAAT
1 TTCATACACAAAT
31031821 TTCAT
1 TTCAT
31031826 TTCATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (13 bp):
TTCATACACAAAT
Found at i:31032304 original size:40 final size:44
Alignment explanation
Indices: 31032260--31032485 Score: 131
Period size: 41 Copynumber: 5.4 Consensus size: 44
31032250 AGGTTCATGT
*
31032260 GTCTTCCTTTTT-AACA-A-TCTTATGCTC-TACCGAGTCATAA
1 GTCTTCCTTTTTAAACATAGTCTCATGCTCATACCGAGTCATAA
** *
31032300 GTCTTCCTTTTTAAACATAGTCTCATGCTCATTTCGAGTCATGA
1 GTCTTCCTTTTTAAACATAGTCTCATGCTCATACCGAGTCATAA
* ** * *
31032344 GTCTTCC--TTTAACACAT--TCTCATTCTCACCCCGAGACATGA
1 GTCTTCCTTTTTAA-ACATAGTCTCATGCTCATACCGAGTCATAA
** * * ** *
31032385 GTCTTCC--TTT-AACATTTTCTCATGTTCCTTTCGAGTCATGA
1 GTCTTCCTTTTTAAACATAGTCTCATGCTCATACCGAGTCATAA
* * * *
31032426 GTCTTCCTTTTATATA-A-ACTCTCATGCTCA-ACCCGAGACATGA
1 GTCTTCCTTTT-TAAACATAGTCTCATGCTCATA-CCGAGTCATAA
*
31032469 GTCTTCC-ATTTAAACAT
1 GTCTTCCTTTTTAAACAT
31032486 CAAGAAATTC
Statistics
Matches: 146, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
39 4 0.03
40 13 0.09
41 60 0.41
42 9 0.06
43 40 0.27
44 19 0.13
45 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (44 bp):
GTCTTCCTTTTTAAACATAGTCTCATGCTCATACCGAGTCATAA
Found at i:31032353 original size:84 final size:83
Alignment explanation
Indices: 31032254--31032485 Score: 251
Period size: 84 Copynumber: 2.8 Consensus size: 83
31032244 CTTCATAGGT
* * * *
31032254 TCATGTGTCTTCCTTTTTAACAA-TCTTATGCTCTA-CCGAGTCATAAGTCTTCCTTTTTAAACA
1 TCATGAGTCTTCCTTTTTAACAACTCTCATGCTC-ACCCGAGACATGAGTCTTCC--TTTAAACA
31032317 TAGTCTCATGCTCATTTCGAG
63 TAGTCTCATGCTCATTTCGAG
* *
31032338 TCATGAGTCTTCC--TTTAACACATTCTCATTCTCACCCCGAGACATGAGTCTTCCTTT-AACAT
1 TCATGAGTCTTCCTTTTTAACA-ACTCTCATGCTCA-CCCGAGACATGAGTCTTCCTTTAAACAT
** * *
31032400 TTTCTCATGTTCCTTTCGAG
64 AGTCTCATGCTCATTTCGAG
31032420 TCATGAGTCTTCCTTTTATATA-AACTCTCATGCTCAACCCGAGACATGAGTCTTCCATTTAAAC
1 TCATGAGTCTTCCTTTT-TA-ACAACTCTCATGCTC-ACCCGAGACATGAGTCTTCC-TTTAAAC
31032484 AT
62 AT
31032486 CAAGAAATTC
Statistics
Matches: 126, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
82 41 0.33
83 5 0.04
84 51 0.40
85 23 0.18
86 6 0.05
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (83 bp):
TCATGAGTCTTCCTTTTTAACAACTCTCATGCTCACCCGAGACATGAGTCTTCCTTTAAACATAG
TCTCATGCTCATTTCGAG
Found at i:31032384 original size:41 final size:42
Alignment explanation
Indices: 31032334--31032485 Score: 134
Period size: 41 Copynumber: 3.7 Consensus size: 42
31032324 ATGCTCATTT
*
31032334 CGAGTCATGAGTCTTCC-TTTAACACATTCTCATTCTCACCC
1 CGAGACATGAGTCTTCCATTTAACACATTCTCATTCTCACCC
** **
31032375 CGAGACATGAGTCTTCC-TTTAACATTTTCTCATGT-TC-CTTT
1 CGAGACATGAGTCTTCCATTTAACACATTCTCAT-TCTCAC-CC
* * * * * * *
31032416 CGAGTCATGAGTCTTCCTTTTATATAAACTCTCATGCTCAACC
1 CGAGACATGAGTCTTCCATTTA-ACACATTCTCATTCTCACCC
31032459 CGAGACATGAGTCTTCCATTTAA-ACAT
1 CGAGACATGAGTCTTCCATTTAACACAT
31032486 CAAGAAATTC
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
40 1 0.01
41 50 0.57
42 6 0.07
43 30 0.34
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCATTTAACACATTCTCATTCTCACCC
Found at i:31039428 original size:17 final size:18
Alignment explanation
Indices: 31039406--31039444 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
31039396 AAATTTATTA
* *
31039406 ATTAAAGTATA-TATATC
1 ATTAAAATATATTAAATC
31039423 ATTAAAATATATTAAATC
1 ATTAAAATATATTAAATC
31039441 ATTA
1 ATTA
31039445 TAAAAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAAATATATTAAATC
Found at i:31039618 original size:89 final size:85
Alignment explanation
Indices: 31039500--31039681 Score: 199
Period size: 86 Copynumber: 2.1 Consensus size: 85
31039490 CATAATTAAG
* * * *
31039500 CCCTTAAACTTTCTCAAAAAAGCAATTAAGCTCAT-C-CTTTTTTTTGCACTCATTTGGGTACTT
1 CCCTCAAACTTTCTCAAAAAAGAAATTAAGCCCATACTCTTTTTTTTGCA--C---TGGATACTT
31039563 AAACTTTCAAAATACATCAAAAAGA
61 AAACTTTCAAAATACATCAAAAAGA
* * *
31039588 CCCTCAAACCTTT-TCAGAAAAAGAAATTAAGCCCCTACTTTTTTTTTTGCACTGGATACTTGAA
1 CCCTCAAA-CTTTCTCA-AAAAAGAAATTAAGCCCATACTCTTTTTTTTGCACTGGATACTTAAA
* *
31039652 CTTTTAAAATGCATCAAAAAGA
64 CTTTCAAAATACATCAAAAAGA
31039674 CCCTCAAA
1 CCCTCAAA
31039682 TTTTTTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
86 38 0.47
88 10 0.12
89 21 0.26
90 1 0.01
91 11 0.14
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (85 bp):
CCCTCAAACTTTCTCAAAAAAGAAATTAAGCCCATACTCTTTTTTTTGCACTGGATACTTAAACT
TTCAAAATACATCAAAAAGA
Found at i:31039792 original size:48 final size:48
Alignment explanation
Indices: 31039725--31039829 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
31039715 TTTATTAAAA
** *
31039725 AATATAAAAAATTAAAATCAATAAAAGTTAT-AAAAATTAT-TAAATTTT
1 AATA-AAAAAATTAAAATC-ATAAAAAATATAAAAAATTATAAAAATTTT
*
31039773 AATAAAAAAATATAAAATCATAAAAAATATAAAAAATTGTAAAAATTTT
1 AATAAAAAAAT-TAAAATCATAAAAAATATAAAAAATTATAAAAATTTT
31039822 -ATAAAAAA
1 AATAAAAAA
31039830 TCGTAAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 16 0.32
48 27 0.54
49 7 0.14
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (48 bp):
AATAAAAAAATTAAAATCATAAAAAATATAAAAAATTATAAAAATTTT
Found at i:31039808 original size:28 final size:27
Alignment explanation
Indices: 31039774--31039877 Score: 95
Period size: 28 Copynumber: 3.7 Consensus size: 27
31039764 TTAAATTTTA
31039774 ATAAAAAAA-TATAAAATCATAAAAAAT
1 ATAAAAAAATTATAAAAT-ATAAAAAAT
*
31039801 AT-AAAAAATTGTAAAAATTTTATAAAAAAT
1 ATAAAAAAATTAT-AAAA---TATAAAAAAT
* * *
31039831 CGTAAAGAAATTATAAAATATATAGAAAT
1 -ATAAAAAAATTATAAAATATA-AAAAAT
31039860 ATAAAAAAATTATAAAAT
1 ATAAAAAAATTATAAAAT
31039878 TTTATAAAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
26 6 0.10
27 4 0.06
28 24 0.39
29 5 0.08
30 9 0.15
31 6 0.10
32 8 0.13
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (27 bp):
ATAAAAAAATTATAAAATATAAAAAAT
Found at i:31039815 original size:19 final size:19
Alignment explanation
Indices: 31039775--31039848 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 19
31039765 TAAATTTTAA
* *
31039775 TAAAAAA-ATATAAAATCA
1 TAAAAAATATAAAAAATCG
*
31039793 TAAAAAATATAAAAAATTG
1 TAAAAAATATAAAAAATCG
*
31039812 TAAAAATTTTATAAAAAATCG
1 TAAAAA--ATATAAAAAATCG
31039833 TAAAGAAATTATAAAA
1 TAAA-AAA-TATAAAA
31039849 TATATAGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.16
19 14 0.31
21 22 0.49
22 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (19 bp):
TAAAAAATATAAAAAATCG
Found at i:31039826 original size:21 final size:20
Alignment explanation
Indices: 31039786--31039885 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 20
31039776 AAAAAAATAT
* *
31039786 AAAATCATAAAAA-ATATAA
1 AAAATTATAAAAATTTATAA
*
31039805 AAAATTGTAAAAATTTTATAA
1 AAAATTATAAAAA-TTTATAA
** *
31039826 AAAATCGTAAAGAAATTATAA
1 AAAATTATAAA-AATTTATAA
* * *
31039847 AATA-TATAGAAATATA-AA
1 AAAATTATAAAAATTTATAA
*
31039865 AAAATTATAAAATTTTATAA
1 AAAATTATAAAAATTTATAA
31039885 A
1 A
31039886 GTCGTAAGAA
Statistics
Matches: 61, Mismatches: 15, Indels: 9
0.72 0.18 0.11
Matches are distributed among these distances:
18 5 0.08
19 24 0.39
20 6 0.10
21 24 0.39
22 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAATTTATAA
Found at i:31039917 original size:59 final size:59
Alignment explanation
Indices: 31039775--31039922 Score: 155
Period size: 59 Copynumber: 2.5 Consensus size: 59
31039765 TAAATTTTAA
* * *
31039775 TAAA-AAAATATAAAATCATAAA-AAATAT-AAAAAATTGTAAAAATTTTATAAAAAATCG
1 TAAAGAAATTATAAAA-AATAAAGAAATATAAAAAAATTATAAAAATTTTAT-AAAAATCG
* * *
31039833 TAAAGAAATTATAAAATATATAGAAATATAAAAAAATTAT-AAAATTTTAT-AAAGTCG
1 TAAAGAAATTATAAAAAATAAAGAAATATAAAAAAATTATAAAAATTTTATAAAAATCG
31039890 T-AAGAAAATTATAAAAAAAATAAAGAAATATAA
1 TAAAG-AAATTAT--AAAAAATAAAGAAATATAA
31039923 CATTCATAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
56 3 0.04
57 14 0.18
58 8 0.10
59 43 0.56
60 9 0.12
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (59 bp):
TAAAGAAATTATAAAAAATAAAGAAATATAAAAAAATTATAAAAATTTTATAAAAATCG
Found at i:31039922 original size:10 final size:9
Alignment explanation
Indices: 31039720--31039867 Score: 61
Period size: 9 Copynumber: 15.8 Consensus size: 9
31039710 TTGTTTTTAT
31039720 TAAAAAATA
1 TAAAAAATA
31039729 TAAAAAAT-
1 TAAAAAATA
*
31039737 TAAAATCA-A
1 TAAAA-AATA
**
31039746 TAAAAGTTA
1 TAAAAAATA
*
31039755 TAAAAATTA
1 TAAAAAATA
***
31039764 TTAAATTTTAA
1 -TAAAAAAT-A
31039775 TAAAAAA-A
1 TAAAAAATA
*
31039783 TATAAAATCA
1 TAAAAAAT-A
31039793 TAAAAAATA
1 TAAAAAATA
*
31039802 TAAAAAATTG
1 TAAAAAA-TA
*
31039812 TAAAAATTTTA
1 TAAAAA--ATA
*
31039823 TAAAAAATCG
1 TAAAAAAT-A
31039833 TAAAGAAAT-
1 TAAA-AAATA
*
31039842 TATAAAATA
1 TAAAAAATA
*
31039851 TATAGAAATA
1 TA-AAAAATA
31039861 TAAAAAA
1 TAAAAAA
31039868 ATTATAAAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
8 16 0.15
9 41 0.39
10 36 0.34
11 12 0.11
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (9 bp):
TAAAAAATA
Found at i:31044787 original size:17 final size:18
Alignment explanation
Indices: 31044750--31044791 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31044740 GGATTGTTAT
31044750 AAATATTTTGATTTTTAA
1 AAATATTTTGATTTTTAA
31044768 AAATATTATT-ATTTTT-A
1 AAATATT-TTGATTTTTAA
31044785 AAATATT
1 AAATATT
31044792 GAAACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 13 0.57
19 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
AAATATTTTGATTTTTAA
Found at i:31048938 original size:43 final size:43
Alignment explanation
Indices: 31048884--31048997 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
31048874 TTTAGATTTT
*
31048884 TTTTAA-TTTTTTTATTTTGTTACTATTTCTGTTTAAAATCAA
1 TTTTAATTTTTTTTATTTTGTTACTATTTCGGTTTAAAATCAA
*
31048926 TTTTAATTTTTTTTATTTTGTTACTATTTCGGTTTAAAATTAA
1 TTTTAATTTTTTTTATTTTGTTACTATTTCGGTTTAAAATCAA
****
31048969 TTTTAATTAAAATTATTTTGTTACTATTT
1 TTTTAATTTTTTTTATTTTGTTACTATTT
31048998 GGAGTTCTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
42 6 0.09
43 59 0.91
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (43 bp):
TTTTAATTTTTTTTATTTTGTTACTATTTCGGTTTAAAATCAA
Found at i:31049612 original size:61 final size:61
Alignment explanation
Indices: 31049511--31049671 Score: 198
Period size: 61 Copynumber: 2.6 Consensus size: 61
31049501 AGGCTAAAAT
* * * * *
31049511 TAAAAAATTTATTTTTTTAAACTGTGATGGGATTTAGTGCCAATCATTAGATGGCCAAAACC
1 TAAAAAAATTATTTTTTT-ATCTGTGATGGGACTTGGTGCCAACCATTAGATGGCCAAAACC
* *
31049573 -AAAAAAATTATTATTTTTATCTGTGATGGGACTTGGTGCCGACCATTAGATGGCCAGAACC
1 TAAAAAAATTATT-TTTTTATCTGTGATGGGACTTGGTGCCAACCATTAGATGGCCAAAACC
* * * *
31049634 TAAGAAAATTATTTTTTTATTTGTAATAGGACTTGGTG
1 TAAAAAAATTATTTTTTTATCTGTGATGGGACTTGGTG
31049672 TTGGCTCAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
61 70 0.81
62 16 0.19
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (61 bp):
TAAAAAAATTATTTTTTTATCTGTGATGGGACTTGGTGCCAACCATTAGATGGCCAAAACC
Found at i:31052080 original size:27 final size:27
Alignment explanation
Indices: 31052050--31052103 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
31052040 AACACTGAAA
*
31052050 AACTAGCTAATTTTGCCGGAATAGATG
1 AACTAGCTAATTTTACCGGAATAGATG
31052077 AACTAGCTAATTTTACCGGAATAGATG
1 AACTAGCTAATTTTACCGGAATAGATG
31052104 CTTAATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (27 bp):
AACTAGCTAATTTTACCGGAATAGATG
Found at i:31053864 original size:17 final size:17
Alignment explanation
Indices: 31053844--31053877 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31053834 TGAATTTTTC
* *
31053844 CTAAATTTTATTTTTAT
1 CTAAATTATAATTTTAT
31053861 CTAAATTATAATTTTAT
1 CTAAATTATAATTTTAT
31053878 TTTTTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
CTAAATTATAATTTTAT
Found at i:31056748 original size:57 final size:57
Alignment explanation
Indices: 31056648--31056761 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
31056638 GTTAATGCCA
* * **
31056648 ATGTTGATCTTAACATTGTTGTGGTATTTGGTGTGACAACTTCAAATAAAACTTTGT
1 ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
* * *
31056705 ATGTTGATCTCAACACTGTTGTGGTATTTTGCATGGCACCTTCAAATAAAACTTTGT
1 ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
31056762 TCTTATGGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.40
Consensus pattern (57 bp):
ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
Found at i:31057619 original size:22 final size:22
Alignment explanation
Indices: 31057586--31057631 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31057576 CTAAATCAAA
* *
31057586 TAAACTCATGATTTGCAGCCAC
1 TAAACTCATGATGTGCAGCAAC
31057608 TAAATCTC-TGATGTGCAGCAAC
1 TAAA-CTCATGATGTGCAGCAAC
31057630 TA
1 TA
31057632 CATGCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (22 bp):
TAAACTCATGATGTGCAGCAAC
Found at i:31060477 original size:20 final size:21
Alignment explanation
Indices: 31060452--31060492 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
31060442 TTAGTAATAC
31060452 TTTTATC-TCAAAAGTG-TTTT
1 TTTTATCAT-AAAAGTGCTTTT
31060472 TTTTATCATAAAAGTGCTTTT
1 TTTTATCATAAAAGTGCTTTT
31060493 GAGAAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTTATCATAAAAGTGCTTTT
Found at i:31063072 original size:51 final size:51
Alignment explanation
Indices: 31062992--31063088 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
31062982 ACAAACTTAG
* * * *
31062992 CCCTCAAATTTTACATATTATATCGATTTAGTCATAATTTTAAAAATTTAA
1 CCCTCAAATTTCACATATTATATCAATTTAATCATAATTCTAAAAATTTAA
*
31063043 CCCTCAAATTTCACAAATATT-T-TCAATTTAATCCTAATTCTAAAAA
1 CCCTCAAATTTCAC--ATATTATATCAATTTAATCATAATTCTAAAAA
31063089 ATTCAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
51 33 0.85
52 1 0.03
53 5 0.13
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (51 bp):
CCCTCAAATTTCACATATTATATCAATTTAATCATAATTCTAAAAATTTAA
Found at i:31063129 original size:21 final size:21
Alignment explanation
Indices: 31063105--31063154 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31063095 AGAAATATAT
* *
31063105 AAAAATATATTAAT-ATTTTA
1 AAAAATATAATAATAAATTTA
31063125 AAAAATATAATAATAAATTTA
1 AAAAATATAATAATAAATTTA
31063146 AAAAATATA
1 AAAAATATA
31063155 CATAGCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATATAATAATAAATTTA
Found at i:31063844 original size:2 final size:2
Alignment explanation
Indices: 31063788--31063826 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
31063778 AAGTTAACCT
31063788 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC ATC -C TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC T
31063827 TTCGTTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:31073825 original size:2 final size:2
Alignment explanation
Indices: 31073818--31073848 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31073808 ATCTCAATTA
31073818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31073849 AAATAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.